Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1410
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21256
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:2700 original size:13 final size:12
Alignment explanation
Indices: 2682--2712 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2672 TAGTTTCTCG
2682 AAAAAAACTCAA
1 AAAAAAACTCAA
*
2694 AAAAAAATTCAA
1 AAAAAAACTCAA
2706 AAAAAAA
1 AAAAAAA
2713 ATTTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAACTCAA
Found at i:2713 original size:13 final size:13
Alignment explanation
Indices: 2682--2726 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
2672 TAGTTTCTCG
*
2682 AAAAAAACTC-AA
1 AAAAAAATTCAAA
2694 AAAAAAATTCAAA
1 AAAAAAATTCAAA
*
2707 AAAAAAATTTGAAA
1 AAAAAAA-TTCAAA
2721 AAAAAA
1 AAAAAA
2727 CTAGTTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 9 0.31
13 9 0.31
14 11 0.38
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:2788 original size:14 final size:13
Alignment explanation
Indices: 2769--2816 Score: 71
Period size: 13 Copynumber: 3.6 Consensus size: 13
2759 TCAAGTTGTG
2769 AAAAAAAATTTGA
1 AAAAAAAATTTGA
2782 AAAAAAAATTGTGA
1 AAAAAAAATT-TGA
2796 AAAAAAAA-TTGA
1 AAAAAAAATTTGA
2808 GAAAAAAAA
1 -AAAAAAAA
2817 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.09
13 19 0.58
14 11 0.33
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:2793 original size:26 final size:27
Alignment explanation
Indices: 2764--2816 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
2754 GGATATCAAG
*
2764 TTGTGAAAAAAAATTTGA-AAAAAAAA
1 TTGTGAAAAAAAAATTGAGAAAAAAAA
2790 TTGTGAAAAAAAAATTGAGAAAAAAAA
1 TTGTGAAAAAAAAATTGAGAAAAAAAA
2817 GAGAGCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (27 bp):
TTGTGAAAAAAAAATTGAGAAAAAAAA
Found at i:9495 original size:10 final size:10
Alignment explanation
Indices: 9479--9536 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
9469 CAACTCCGAC
9479 CAGCTCAATT
1 CAGCTCAATT
* *
9489 GAGCTCATTT
1 CAGCTCAATT
9499 CAGCTCAA-T
1 CAGCTCAATT
9508 CGAGCTCAATT
1 C-AGCTCAATT
*
9519 TAGCTACAATT
1 CAGCT-CAATT
9530 CAGCTCA
1 CAGCTCA
9537 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:9502 original size:20 final size:20
Alignment explanation
Indices: 9479--9539 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
9469 CAACTCCGAC
9479 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
9499 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
9520 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
9540 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:10811 original size:11 final size:10
Alignment explanation
Indices: 10795--10824 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
10785 GTTCGTAACA
10795 AAAAAAAAGTC
1 AAAAAAAA-TC
10806 AAAAAAAATC
1 AAAAAAAATC
10816 AAAAAAAAT
1 AAAAAAAAT
10825 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:10919 original size:13 final size:13
Alignment explanation
Indices: 10901--10938 Score: 62
Period size: 12 Copynumber: 3.1 Consensus size: 13
10891 AAAAGAGAAG
10901 AAATTCAAAAAAA
1 AAATTCAAAAAAA
10914 AAATTC-AAAAAA
1 AAATTCAAAAAAA
10926 AAA-TCAAAAAAA
1 AAATTCAAAAAAA
10938 A
1 A
10939 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 16 0.67
13 6 0.25
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:10925 original size:12 final size:12
Alignment explanation
Indices: 10901--10938 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
10891 AAAAGAGAAG
10901 AAATTCAAAAAAA
1 AAATTC-AAAAAA
10914 AAATTCAAAAAA
1 AAATTCAAAAAA
10926 AAA-TCAAAAAA
1 AAATTCAAAAAA
10937 AA
1 AA
10939 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 10 0.40
12 9 0.36
13 6 0.24
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:10994 original size:12 final size:12
Alignment explanation
Indices: 10908--10995 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 12
10898 AAGAAATTCA
* *
10908 AAAAAAAAATTC
1 AAAAAAAAAGTG
10920 AAAAAAAAA-T-
1 AAAAAAAAAGTG
*
10930 CAAAAAAAA--G
1 AAAAAAAAAGTG
10940 AAAAAAAAAGTG
1 AAAAAAAAAGTG
10952 ACAAAAAAATCGAGT-
1 A-AAAAAAA---AGTG
* *
10967 TAAAAAAAAGAAG
1 AAAAAAAAAG-TG
10980 AAAAAAAAAGTG
1 AAAAAAAAAGTG
10992 AAAA
1 AAAA
10996 GTCTTGCGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
10 16 0.26
11 3 0.05
12 16 0.26
13 16 0.26
14 7 0.11
16 3 0.05
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.09
Consensus pattern (12 bp):
AAAAAAAAAGTG
Found at i:12004 original size:18 final size:18
Alignment explanation
Indices: 11978--12015 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11968 AAATTGAAAG
11978 AAAACAAAAAGAAAACAA
1 AAAACAAAAAGAAAACAA
* *
11996 AAAAGAAAAAGAAATCAA
1 AAAACAAAAAGAAAACAA
12014 AA
1 AA
12016 TAGTGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.03
Consensus pattern (18 bp):
AAAACAAAAAGAAAACAA
Found at i:12015 original size:11 final size:12
Alignment explanation
Indices: 11974--12004 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11964 AAAGAAATTG
11974 AAAGAAAAC-AA
1 AAAGAAAACAAA
11985 AAAGAAAACAAA
1 AAAGAAAACAAA
11997 AAAGAAAA
1 AAAGAAAA
12005 AGAAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAGAAAACAAA
Found at i:12069 original size:18 final size:18
Alignment explanation
Indices: 12048--12082 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12038 AGAAAAGAAA
12048 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
12066 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
12083 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Done.